The only place I'd argue is that dilithium crystals were obviously needed to use warp drive, too. Your diagram would indicate that even without crystals, the ship could initiate warp, but I believe the original show directly contradicts that in several episodes.
Well, the nacelles are huge: plenty of room for a couple of big dilithium crystals in-line.
However, the show is unfortunately inconsistent in its use of dilithium. It had to be established as something essential to starships. It had to be really valuable, like an essential fuel, so as to justify the drama of some episodes.
So not only did we see engineering crew handling them in a way that implies they're used on the interior of the ship, but it's also implied that these same crystals control whether the engines run.
As I say, the show was a bit vague, probably because they had a show to do every week, and working out all the minutia was simply impossible. It was amazing that they were as consistent as they were.
Anyway, I'm not sure how you justify it, other than making the crystals integral to both shipboard and warp drive systems. That implies multiple locations for crystals: one in each nacelle; the energizer room; and I think sticking out of that "overhead cam device" doohickey in the middle of the engine room in "Elaan Of Troyus".
If crystals were sort of power regulators, it might make sense to have them several places. On the other hand, one starts to wonder just how rare they are if Starfleet can throw them all over the ship like that.
As I say, one of those things that just wasn't handled consistently. Dilithium crystals were unfortunately more a plot device than anything else. They'd need more whenever the plot demanded the ship be some level of crippled.
Maybe the crystals they always worried about were there in the engine room, in the doohickey in the floor? Perhaps they're some kind of "circuit breaker" or "spark plug", without which they can't make the engines start?
I know, I'm grasping. Blame Matt Jeffries et al for never envisioning we'd be arguing about it 50 years later.
One thing I do know: he meant that the real power of the ship and all its really dangerous components were in the nacelles. As you say, if you just look at the visuals, it's obvious: we're seeing the annihilation effect right through the nacelle caps!